HGNC Approved Gene Symbol: RAP1B
Cytogenetic location: 12q15 Genomic coordinates (GRCh38): 12:68,610,899-68,671,901 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 12q15 | Thrombocytopenia 11 with multiple congenital anomalies and dysmorphic facies | 620654 | Autosomal dominant | 3 |
RAP1B and RAP1A (179520) belong to a superfamily of RAS (see 190020)-like small GTP-binding proteins involved in cell signaling.
Pizon et al. (1988) cloned human RAP1B. The deduced 184-amino acid protein is 95% identical to RAP1A. RAP1B shares several properties with the RAS protein, suggesting that it may bind GTP/GDP and have a membrane location.
Matsui et al. (1990) reported the amino acid sequence of RAP1B, which they called SMG p21B, purified from bovine brain and human platelets. The bovine and human proteins are identical.
Hoshijima et al. (1988) and Kawata et al. (1989) reported that RAP1B is phosphorylated by cAMP-dependent protein kinase (see 601639) on ser179. Kawata et al., 1990 found that phosphorylation enhanced GDP/GTP exchange.
Kawata et al. (1990) determined that purified human platelet RAP1B is posttranslationally modified by the geranylgeranylation of cys181. Further modifications cause proteolytic removal of the last 3 C-terminal amino acids, followed by partial methylation of the remaining terminal cysteinyl carboxyl group. Kawata et al. (1990) suggested that geranylgeranylation and methylation of RAP1B are important, because they found that C-terminal modification was required for the binding of RAP1B to membranes.
Lova et al. (2003) noted that, in resting cells, RAP1B is mainly located at the membrane, but translocates to the cytosol upon activation. In activated platelets, RAP1B interacts with the reorganized actin-based cytoskeleton. RAP1B is activated by phosphorylation, increased intracellular Ca(2+), and by agonist-induced stimulation of Gi (139310), which results in the rapid binding of GTP to RAP1B. Lova et al. (2003) found that stimulation of Gi-dependent signaling could activate human platelet RAP1B through phosphatidylinositol(3,4,5)-trisphosphate (PtdIns(3,4,5)P3), but not PtdIns(3,4)P2. They concluded that the PI3 kinase (see 601232) pathway of RAP1B activation may contribute to potentiation of platelet aggregation.
Schwamborn and Puschel (2004) found that localization of Rap1b to the tip of a single neurite in rat hippocampal neurons was a decisive step in determining which neurite became the axon.
By in situ hybridization, Rousseau-Merck et al. (1990) mapped the RAP1B gene to chromosome 12q14.
Crystal Structure
Rehmann et al. (2008) determined the structure of EPAC2 (606058) in complex with a cAMP analog (Sp-cAMPS) and RAP1B by x-ray crystallography and single-particle electron microscopy. The structure represents the cAMP-activated state of the EPAC2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation revealed that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site toward a docking site at the Ras exchange motif domain.
Thrombocytopenia 11 with Multiple Congenital Anomalies and Dysmorphic Facies
In 2 unrelated patients with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Niemann et al. (2020) identified de novo heterozygous missense mutations in the RAP1B gene (G12V, 179530.0002 and G60R, 178G-C, 179530.0003). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were not present in public databases. Functional studies of the variants and studies of patient cells were not performed, but molecular modeling based on similar variations in other RAS-related genes (see, e.g., KRAS; 190070) predicted that the variants would cause conformational changes of the GTPase domain and result in constitutive activation with a gain-of-function effect through dysregulation of the downstream MEK/ERK signaling pathway (see 176872). The authors noted that studies in mice have demonstrated a link between Rap1b and platelet function (see ANIMAL MODEL).
In a 23-year-old man with THC11, Miller et al. (2022) identified a de novo heterozygous missense mutation in the RAP1B gene (A59G; 179530.0004). The mutation, which was found by genome sequencing, was not present in the gnomAD database. It occurred at a conserved residue in the switch II domain important for GTP hydrolysis. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a gain-of-function effect with increased downstream signaling based on similarities to other RAS family proteins. Miller et al. (2022) concluded that the RAP1B-related syndromic thrombocytopenia phenotype can be considered a RASopathy.
In 2 unrelated patients with THC11, Pardo et al. (2024) identified heterozygous missense mutations in the RAP1B gene (G12E, 179530.0005 and G60R, c.178G-A, 179530.0006). An additional search in the DECIPHER database identified a female patient (patient 323 709) with intellectual disability and a heterozygous missense variant in the RAP1B gene (c.179G-T, G60V) that affected the switch II region; no hematologic abnormalities were reported in this patient. The authors noted that RAP1B variants associated with syndromic thrombocytopenia cluster into 2 hotspots with similar gain-of-function effects. Variants affecting residue Gly12 in the P-loop are predicted to inactivate RAP1B GTPase activity, leading to constitutively active GTP-bound RAP1B. Mutations affecting residues Ala59 and Gly60 map to the switch II region involved in the interaction between RAP1B and cognate GTPase activating proteins (GAPs), which likely render RAP1B resistant to GAP-dependent regulation, resulting in increased levels of the active RAP1B-GTP isoform.
Associations Pending Confirmation
For discussion of a possible association between variation in the RAP1B gene and Kabuki syndrome (147920), see 179530.0001.
Chrzanowska-Wodnicka et al. (2005) generated Rap1b -/- mice and observed a bleeding defect due to defective platelet function. Aggregation of Rap1b-null platelets was reduced in response to stimulation with both G protein-coupled receptor (GPCR; see 600239)-linked and GPCR-independent agonists and was found to be due to decreased agonist-induced activation of integrin alpha-IIb-beta-3 (see 607759, 173470) and signaling downstream. In vivo, Rap1b-null mice were protected from arterial thrombosis. Chrzanowska-Wodnicka et al. (2005) concluded that RAP1B is involved in a common pathway of integrin activation, is required for normal hemostasis in vivo, and may be a clinically relevant antithrombotic therapy target.
Stefanini et al. (2018) found that mice with megakaryocyte-specific Rap1a and Rap1b double-knockout were viable, fertile, and healthy, with no spontaneous bleeding, but that they developed macrothrombocytopenia. Loss of Rap1a and Rap1b led to 80 to 90% inhibition of integrin activation. The lack of complete platelet integrin activation in the absence of Rap1a and Rap1b was due to limited integrin activation mediated by Talin1 (186745), but not by other Rap proteins, such as Rap2 GTPases, also expressed in platelets. Further analysis showed that Rap isoforms had redundant and isoform-specific functions in platelets and were important for platelet spreading, clot contraction, release of second-wave mediators, platelet adhesion, and formation of thrombotic and hemostatic plugs. However, Rap1 signaling in platelets was dispensable for vascular integrity during development and at sites of inflammation.
This variant is classified as a variant of unknown significance because its contribution to a Kabuki-like syndrome (see 147920) has not been confirmed.
In a boy, born of unrelated Turkish parents, with features reminiscent of Kabuki syndrome, Bogershausen et al. (2015) identified a de novo heterozygous c.451A-G transition in the RAP1B gene, resulting in a lys151-to-glu (K151E) substitution at a conserved residue close to the GTP-binding site of RAP1B. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the Exome Variant Server or ExAC databases. Expression of the mutation in rap1b-null zebrafish failed to rescue convergent-extension (CE) defects, consistent with a loss of function. There was no evidence for a dominant-negative effect; thus the mutation likely resulted in haploinsufficiency. The patient had growth defects with short stature and microcephaly, developmental delay, seizures, congenital heart defects, and dysmorphic facial features, including long palpebral fissures, arched eyebrows, long eyelashes, dysplastic ears, and strabismus. He also had right tibial shortening and brachyphalangy. The patient had initially been diagnosed clinically with Hadziselimovic syndrome (612946).
In a 36-year-old woman (case 1), born of unrelated parents, with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Niemann et al. (2020) identified a de novo heterozygous c.35G-T transversion (c.35G-T, NM_001010942.2) in the RAP1B gene, resulting in a gly12-to-val (G12V) substitution at a highly conserved residue in the P-loop of the catalytic RAP1B domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not present in public databases. Functional studies of the variant and studies of patient cells were not performed, but molecular modeling and known variations at this residue in other RAS-related proteins predicted that the G12V mutation would cause a conformational change of the GTPase domain and result in a gain-of-function effect with dysregulation of the downstream MEK/ERK signaling pathway (see 176872).
In a 13-year-old boy (case 2), born of unrelated parents, with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Niemann et al. (2020) identified a de novo heterozygous c.178G-C transversion (c.178G-C, NM_001010942.2) in the RAP1B gene, resulting in a gly60-to-arg (G60R) substitution at a highly conserved residue in the GTPase domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not present in public databases. Functional studies of the variant and studies of patient cells were not performed, but molecular modeling and known variations at this residue in other RAS-related proteins predicted that the mutation would cause a conformational change of the GTPase domain and result in a gain-of-function effect with dysregulation of the downstream MEK/ERK pathway (see 176872).
In a 23-year-old man with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Miller et al. (2022) identified a de novo heterozygous c.176C-G transversion (c.176C-G, NM_001010942) in the RAP1B gene, resulting in an ala59-to-gly (A59G) substitution at a conserved residue in the switch II domain important for GTP hydrolysis. The mutation, which was found by genome sequencing, was not present in the gnomAD database. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to result in a gain-of-function effect with increased downstream signaling based on similarities to variants in other RAS family genes (see, e.g., KRAS, 190070).
In a 16-year-old girl (case 1) with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Pardo et al. (2024) identified a de novo heterozygous c.35G-A transition (c.35G-A, NM_001010942.2) in exon 2 of the RAP1B gene, resulting in a gly12-to-glu (G12E) substitution in the P-loop of the GTP-binding domain. Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to inactivate RAP1B GTPase activity, leading to constitutively active GTP-bound RAP1B and a gain-of-function effect.
In a 5-year-old boy (case 2) with thrombocytopenia-11 with multiple congenital anomalies and dysmorphic facies (THC11; 620654), Pardo et al. (2024) identified heterozygosity for a c.178G-A transition (c.178G-A, NM_001010942.2) in the RAP1B gene, resulting in a gly60-to-arg (G60R) substitution in the switch II region that is essential for the interaction with GTPase activating proteins (GAPs). Functional studies of the variant and studies of patient cells were not performed, but the variant was predicted to render RAP1B resistant to GAP-dependent regulation, resulting in increased levels of the active RAP1B-GTP isoform and a gain-of-function effect.
Bogershausen, N., Tsai, I. C., Pohl, E., Kiper, P. O., Beleggia, F., Percin, E. F., Keupp, K., Matchan, A., Milz, E., Alanay, Y., Kayserili, H., Liu, Y., and 16 others. RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome. J. Clin. Invest. 125: 3585-3599, 2015. [PubMed: 26280580] [Full Text: https://doi.org/10.1172/JCI80102]
Chrzanowska-Wodnicka, M., Smyth, S. S., Schoenwaelder, S. M., Fischer, T. H., White, G. C., II. Rap1b is required for normal platelet function and hemostasis in mice. J. Clin. Invest. 115: 680-687, 2005. Note: Erratum: J. Clin. Invest. 115: 2296 only, 2005. [PubMed: 15696195] [Full Text: https://doi.org/10.1172/JCI22973]
Hoshijima, M., Kikuchi, A., Kawata, M., Ohmori, T., Hashimoto, E., Yamamura, H., Takai, Y. Phosphorylation by cyclic AMP-dependent protein kinase of a human platelet Mr 22,000 GTP-binding protein (smg p21) having the same putative effector domain as the ras gene products. Biochem. Biophys. Res. Commun. 157: 851-860, 1988. [PubMed: 2849942] [Full Text: https://doi.org/10.1016/s0006-291x(88)80953-7]
Kawata, M., Farnsworth, C. C., Yoshida, Y., Gelb, M. H., Glomset, J. A., Takai, Y. Posttranslationally processed structure of the human platelet protein smg p21B: evidence for geranylgeranylation and carboxyl methylation of the C-terminal cysteine. Proc. Nat. Acad. Sci. 87: 8960-8964, 1990. [PubMed: 2123345] [Full Text: https://doi.org/10.1073/pnas.87.22.8960]
Kawata, M., Kikuchi, A., Hoshijima, M., Yamamoto, K., Hashimoto, E., Yamamura, H., Takai, Y. Phosphorylation of smg p21, a ras p21-like GTP-binding protein, by cyclic AMP-dependent protein kinase in a cell-free system and in response to prostaglandin E1 in intact human platelets. J. Biol. Chem. 264: 15688-15695, 1989. [PubMed: 2504724]
Lova, P., Paganini, S., Hirsch, E., Barberis, L., Wymann, M., Sinigaglia, F., Balduini, C., Torti, M. A selective role for phosphatidylinositol 3,4,5-trisphosphate in the Gi-dependent activation of platelet Rap1B. J. Biol. Chem. 278: 131-138, 2003. [PubMed: 12407113] [Full Text: https://doi.org/10.1074/jbc.M204821200]
Matsui, Y., Kikuchi, A., Kawata, M., Kondo, J., Teranishi, Y., Takai, Y. Molecular cloning of smg p21B and identification of smg p21 purified from bovine brain and human platelets as smg p21B. Biochem. Biophys. Res. Commun. 166: 1010-1016, 1990. [PubMed: 2105724] [Full Text: https://doi.org/10.1016/0006-291x(90)90911-6]
Miller, D., Saeed, A., Nelson, A. C., Bower, M., Aggarwal, A. Third reported patient with RAP1B-related syndromic thrombocytopenia and novel clinical findings. Am. J. Med. Genet. 188A: 2808-2814, 2022. [PubMed: 35451551] [Full Text: https://doi.org/10.1002/ajmg.a.62760]
Niemann, J. H., Du, C., Morlot, S., Schmidt, G., Auber, B., Kaune, B., Gohring, G., Ripperger, T., Schlegelberger, B., Hofmann, W., Smol, T., Ait-Yahya, E., Raimbault, A., Lambilliotte, A., Petit, F., Steinemann, D. De novo missense variants in the RAP1B gene identified in two patients with syndromic thrombocytopenia. Clin. Genet. 98: 374-378, 2020. [PubMed: 32627184] [Full Text: https://doi.org/10.1111/cge.13807]
Pardo, L. M., Aanicai, R., Zonic, E., Hakonen, A. H., Zielske, S., Bauer, P., Bertoli-Avella, A. M. Adding to the evidence of gene-disease association of RAP1B and syndromic thrombocytopenia. Clin. Genet. 105: 196-201, 2024. [PubMed: 37850357] [Full Text: https://doi.org/10.1111/cge.14438]
Pizon, V., Lerosey, I., Chardin, P., Tavitian, A. Nucleotide sequence of a human cDNA encoding ras-related protein (rap1B). Nucleic Acids Res. 16: 7719 only, 1988. [PubMed: 3137530] [Full Text: https://doi.org/10.1093/nar/16.15.7719]
Rehmann, H., Arias-Palomo, E., Hadders, M. A., Schwede, F., Llorca, O., Bos, J. L. Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B. Nature 455: 124-127, 2008. [PubMed: 18660803] [Full Text: https://doi.org/10.1038/nature07187]
Rousseau-Merck, M. F., Pizon, V., Tavitian, A., Berger, R. Chromosome mapping of the human RAS-related RAP1A, RAP1B, and RAP2 genes to chromosomes 1p12-p13, 12q14, and 13q34, respectively. Cytogenet. Cell Genet. 53: 2-4, 1990. [PubMed: 2108841] [Full Text: https://doi.org/10.1159/000132883]
Schwamborn, J. C., Puschel, A. W. The sequential activity of the GTPases Rap1B and Cdc42 determines neuronal polarity. Nature Neurosci. 7: 923-929, 2004. [PubMed: 15286792] [Full Text: https://doi.org/10.1038/nn1295]
Stefanini, L., Lee, R. H., Paul, D. S., O'Shaughnessy, E. C., Ghalloussi, D., Jones, C. I., Boulaftali, Y., Poe, K. O., Piatt, R., Kechele, D. O., Caron, K. M., Hahn, K. M., Gibbins, J. M., Bergmeier, W. Functional redundancy between RAP1 isoforms in murine platelet production and function. Blood 132: 1951-1962, 2018. [PubMed: 30131434] [Full Text: https://doi.org/10.1182/blood-2018-03-838714]